Stargate Atlantis: S7--The Species Divide
by the morrighan
Summary: The war rages on and the differences between the species are revealed...or are they? This is the 3rd story of 5.
1. Chapter 1

Stargate Atlantis: S7—The Species Divide

Greed.

Colonel John Sheppard knew it was wrong, but it couldn't be helped. He wanted them all. He wanted every one of these bastards gone, no, not just gone but dead and gone. He wanted to eliminate them; no he wanted to annihilate them from this galaxy. He wanted this species of human extinct, like it was back in the Milky Way galaxy.

And he wanted one of their ships.

The power was phenomenal. Even in the midst of battle John could only wonder at the raw power these aliens possessed. Their weaponry was cutting a swathe through his ranks, erasing his allies as easily as if they were just chalk on a blackboard. Space was lit by the furious crisscrossing of laser beams, red and green and yellow spumes that created more explosions and bombarded the shields of vessels with lilac bursts.

The initial scouting party had morphed into an invasion force. This new species from another galaxy had to be stopped now, and stopped here at the doorstep to the Pegasus galaxy. To John it seemed to be yet another mess that the Ancients had created and then never resolved; the same as the Wraith and the Replicators. John was getting tired of cleaning up after the Ancients.

"Hard to port! How're the shields?" John shouted, as yet another hit caused the _Tria _to shake. He glanced at the data pad hooked to his command chair. Words were splayed across it, a jumble of nonsense until the translation program began to replace with them with English. It was still a disjointed mess and John had to study it to make sense of it all.

Words fell into place but it took a few minutes for an actual sentence to form in his mind and then on the screen. Some words remained untranslated. John could only guess at their meanings.

"We're at seventy percent, sir!"

"Weapons! Target their fighter bays! Clear the road!"

John was loath to commit his Jumpers to the fray just yet. The Fuglies weren't deploying their single fighter ships yet either. The motley fleet allied with Atlantis was having some success so far against the enemy with harrying attacks, distracting the larger vessels from the Wraith Hives and the _Tria. _ John found himself running interference between the Fugly ships and his allies. It was not a position he had intended upon taking but he took it nonetheless, seeing the necessity.

Simply put the other vessels were no match for the Fugly ships.

"Colonel Sheppard! We've got updates!"

"On screen! Share with the class!" John swerved to view a larger screen. It showed the Fugly ships slowly retreating under the barrage from the larger vessels at his command. But there were still too many. Too many. They were still outnumbered.

"Casualties?"

"Two Traveler ships, two Genii, one Alliance vessel, a Wraith Hive. The _Aegis_ is sustaining significant damage."

"Shit. We need to take out the leader and take him out now!" John swerved back and eyed the data pad. As the Fuglies talked to each other John could glean their next moves and counter them effectively. So far it was working, but the sheer firepower of the enemy was a negating factor. Trying to figure out their agenda was another can of worms. How did you interpret an alien species and their motives, apart from the obvious one of staying alive?

For a moment he regretted his decision not to have Moira on board with him. If anyone could discern the way these aliens thought it would be her. But his regret disappeared. He wouldn't risk her like that. The alien interface had done enough damage to her mind and she was almost recovered now. He wouldn't risk harming her in any way.

He drummed his fingers on the armrest, reading and waiting and glancing up as another hit rocked the ship. His eyes darted from screen to screen to viewport to data pad until a pattern emerged. It was a pattern he could discern and understand at last. He recognized military maneuvers when he saw them—even alien ones.

"Shields at sixty-five, sir!"

"Correct to this heading! Open a channel to Todd!" John's fingers moved across the controls. "Todd, follow my lead! We're gonna take out the leader on my mark! Got it? Let's go!"

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The Wraith Hive was rocked by another explosive blast of energy. Alarms wailed but the shields were holding, at least so far. Lights flickered and the ship seemed to groan. It was partly organic and Todd wondered if the vessel could feel or even comprehend pain.

The Wraith had been loath to join this fight, to ally with Atlantis at all but they had seen the necessity. United under one queen the Wraith had been growing in power until the appearance of these strange new aliens. According to the Lantean scientists the aliens were human, but a different species of human. Whatever they were the Wraith were unable to feed upon them. Thus they were useless and should be eliminated; especially as they were destructive and possessed technology even beyond that of Atlantis.

Sheppard's barking orders interrupted his musings and Todd snarled. "Do you think that is wise, John Sheppard? We would be in a precarious position and separated from the rest of the fleet."

"I know that!" John's voice crackled over the com unit, irate and loud. "It's our only chance to begin to even the odds. They are protecting that ship so we have to destroy it!"

"And how would you know that?"

"Trust me, I know it!"

"Very well." Todd gestured. The Wraith ship swerved and began to follow after the Ancient warship commanded by their human ally. Realistically they were the only chance against these enemies, and both knew it. The outcome of the battle would be decided by only a handful of ships. Todd intended to be on the winning side no matter what. "Status?"

"Shields are at sixty percent. We've sustained some minimal damage to the hull. Should we release the Darts?"

"Not yet. Prime our weapons and stand by. Order the rest of the Hives to hold back and maintain position. For now we will allow John Sheppard to run this mission."

"The Queen's orders were to—"

"I know what the Queen's orders were! Stand by!" Todd snarled, rising to his feet. The two Wraith stared at each other. For a moment the silence was fraught with tension. Finally the second in command nodded and turned back to his console. Todd's hands were curled into fists. He glanced round the ship as it was rocked again. Whatever weapons these new aliens had they were more dangerous than any that the Ancients had used.

He could not let this kind of technology fall into the hands of the Lanteans.

Particularly not into the hands of John Sheppard.

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"Fall back! All ships fall back!" Colonel Abraham Ellis shouted as the barrage of firepower was almost blinding. The explosions were creating a curtain of gas that was becoming difficult to see through and playing havoc with the systems. The shields were holding but power was draining quickly. The Asgard ship was tough but it was not indestructible. "Sheppard! We need to deploy out fighters now!"

"Negative!" snarled the voice of the military commander. "Do not engage them like that! If those fighters get near they will attempt to board!"

"I'll take the chance! We need more—"

"Negative! You will not deploy the F-302s!"

Abraham cursed and swerved in his command chair. He cut off the communications. Quickly he surveyed the consoles, assessing the systems and power levels. "Fire missiles now! Target those firing tubes! And get those bays ready to launch!"

"Sir?"

"You heard! We're getting pulverized out here like this! We need to engage ship to ship so we can create a feint and take of the big ones out! All pilots to your ships!" He was not going to let some wet behind the ears lieutenant colonel lose the battle for him. It was ridiculous that John Sheppard was in charge in the first place. The man had never been in charge of a fully armed spaceship or a complicated space battle.

Ronon Dex placed a heavy hand on the colonel's shoulder. He did not like his friend's orders being countermanded, especially not by a man who was not of Atlantis. "Sheppard said not to engage."

Abraham glanced up at the towering Satedan. "This is my ship and this is my call." He shrugged off the restraining hand and turned back to the viewport. "Take us out far enough to deploy fighters. Then let's target one of those big ones."

Ronon shook his head. "You're making a mistake."

"It's my mistake to make!"

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John couldn't keep still in the command chair. Finally he stood, moving behind it to keep an eye on the data pad as the translations scrolled along, giving him the intel he needed. "Open Channel W," he ordered. At the technician's nod he said, "Todd, follow this vector. We need to clear the way and head for that ship in the middle."

"What is so special about that ship, John Sheppard?"

"I dunno, but the chatter is all about it."

"What chatter? Ah…the trick up your sleeve?"

"One of them, yeah." John cut off the transmission with a gesture. "Shields forward, at maximum." The translation program was a closely guarded secret, and John intended to keep it that way.

His gaze narrowed as the ship veered and doggedly maintained its course towards the most protected ship in a fleet of ships that were all firing simultaneously. The darkness of space was intercut but gaseous bubbles of blue and violet. Red and green and yellow lasers cut the void with violent patterns. Explosions careened on every side. The _Tria's_ shield was constantly being bombarded and it became a visible pinkish hue around the ship.

John could imagine the sounds of the explosions and the cutting lasers but he knew that in space all was silence.

Out here on the edge of the galaxy there were no planets. There was no Stargate. In other words there was no escape except for a hyperspace window. If any ship was damaged and unable to fly there was no place for it to land. There was no safe harbor out this far.

The nearest safe place was Echo Base and at sublight the haven was two weeks out. It was a tiny dot with its slightly larger twin planet in an ocean of overwhelming blackness and emptiness. John wondered why the Ancients had placed a Stargate on that planet in the first place. Maybe they had known that someday the Fuglies would launch an invasion force.

"Sir? We're being hailed."

"Patch it through! This is Sheppard!"

"Sheppard? Our ships can't take much more of this!"

John glanced at the console. The Genii commander appeared harried. Smoke billowed behind him. His sharply cut gray uniform was stained with grease and sweat. Behind him his crew appeared equally harried and desperate. "Understood. Just give me enough time to reach that ship and then you can fall back."

"Sheppard, we're taking too many hits!" wailed the voice of Larrin.

"Just hang in there! I need more time to finish this!" John stated. He glanced at a star chart. His numbers were dwindling as damaged ships retreated and were out of the battle. A few wrecks were floating harmlessly, creating more obstacles in his path.

"Sir, I'm detecting fighters! Ours not theirs!"

"What? What the…sonuvabitch!" John slammed his hand on the com unit. Power flared in the ship, reacting to his ATA gene. "Ellis! What the hell are you doing?"

"Trying to even the odds!"

John stared. Wave after wave of single ships was being vomited from the larger Fugly vessels. Suddenly the battle had accelerated into a single man combat situation. "Maintain course," he said quietly, as anger was a grim tide inside him. He would deal with Ellis later, and all of those causalities would be on the other man's shoulders.

Even now he could see that the F302s were no match for the Fugly single fighters. Although the F302s had more maneuverability the Fugly fighters were faster and had more firepower. The triangular ships were more streamlined and the wings could unfold to reveal a double array of weaponry.

John knew it would be pointless to argue and the last thing they needed was a shouting match. Everyone needed to concentrate on the battle, not on two at odds colonels.

Smaller ships were exploding and spinning all around them now, like some space circus show. John ignored them and concentrated on his target. He glanced at the translation screen, watching the gibberish turn into words, into sentences that gave him a reasonable idea of what they were planning.

What he saw gave him the chills.


	2. Chapter 2

Stargate Atlantis: S7—The Species Divide2

"It's impossible." Doctor Rodney McKay sat back from the console and ran a hand through his thinning hair. He had been working for several hours. His sandwich lay untouched on a plate near him, indicating the severity of the situation. If Rodney wasn't interested in food then things were very serious indeed. "The distances are too great. Even Echo Base can't get an exact lock on them. They can monitor the battle but they can't discern which ship is which, and the radio chatter is sporadic. Long range sensors are being rendered useless. We're just going to have to wait it out."

Richard Woolsey frowned as he stood behind the tired physicist. The screen was vacant except for the faint blips that represented the distant battle. Dots on a screen told him nothing about what was happening. "Very well. If Echo Base picks up anything significant they will relay it here. You've done all you can, Rodney. All we can do is wait."

"I know." Rodney sighed and glared at the screen. "I don't like waiting."

"So far our scans show no ships anywhere near Atlantis," Doctor Radek Zelenka commented. The Czech physicist adjusted his glasses on the bridge of his nose.

"Keep scanning, just in case. I don't want any surprises," Richard noted. He clasped his hands behind his back. He hated waiting as much as everyone else.

"Has there been any word from our allies?" Teyla Emmagan asked. She glanced at the consoles but they told her nothing. She had hated being left behind but knew that if anything threatened Atlantis she would be of more use here.

"We've gotten plenty of that! Requests for updates and such, but we don't have anything to give them," Amelia Banks-Dex answered. She frowned at her computer, worrying as always about her husband. He was on the _Aegis _and in the midst of the battle. She would rather have been out there instead of stuck behind a console in Atlantis.

"I had thought of inviting the leaders of our respective allies to wait here with us but decided against it," Richard explained. "Since only half of them honored their commitment to us I think it's best that we filter all incoming information."

"And it's not like you can invite the Wraith," Amelia joked.

Rodney and Richard exchanged a glance. Only a few knew that the Wraith's new queen was a strange amalgamation of Elizabeth Weir's genetics and memories cloned from her Replicator and then joined to a Wraith queen. She was the most dangerous entity out there. The only advantage that Atlantis had was that she did not know the new location of the city.

At least not yet.

Rodney resumed staring at a data screen. He drummed his fingers along the console in an unconscious imitation of the military commander. "I think I should take a Jumper out there."

"What? Out to the battle?"

"No. Well, sort of." Rodney met Richard's surprised expression. "Out to Echo Base. I can help boost their sensors and get a better read on what's happening out there. With Gate access I can be there and back in no time," he added, forestalling the expedition leader's objections. "It will give us a clearer picture of what's going on."

"You know that the Gate isn't working very well on Echo Base, and travel through it is risky at the best of times," Radek cautioned. "And these are certainly not the best of times."

"And you are going to fly the Jumper?" Richard asked.

"Yes. I've flown a Jumper before, you know!" Rodney snarled, indignant.

"You have not flown so far, and through an unstable wormhole," Teyla gently reminded. "We are all worried. We must give Colonel Sheppard and our allies time to succeed."

"I agree. You are more needed here, Rodney, especially if any danger comes our way," Richard agreed. "You said it yourself. The _Tria_ is more than capable to handle whatever the Fuglies throw its way."

"Yes, I know that!" Rodney snapped. "I upgraded all the weaponry and even put in a special surprise should they choose to engage their Penning trap. But still…" His words fell away as he stared at the screen in front of him.

The dots blinked and blinked and blinked.

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Doctor Moira Sheppard swore as she adjusted the headphones. She was leaning forward in her chair, eyes glued to the monitor in front of her. Garbled voices sounded tinny, and too far away to grasp. Static crackled wildly and tingled in her ears. She sighed.

She strained to listen for any sound, but in particular for the cadences of her husband John Sheppard. Only static tickled her ears and she silently swore. A tap on her shoulder made her look up and slide the headphones off her.

"Anything yet?" Doctor Chris Sands asked. The leader of the Echo Base scientific survey group was concerned, although he tried not to show it. This battle was occurring in his backyard, so to speak, and the outpost has little in the way of either weaponry or defensive capabilities.

"No. I can hear only bits and pieces of jumbled dialogue."

"Theirs or ours?"

"Both." She tapped a few keys. "This is the last transmission the scanner could detect before the interference. John…I mean Colonel Sheppard was ordering the ships into position." Moira pointed to the screen. She recalled the sound of John's voice, the tone of command. She tried to suppress the ever-present worry. "Can you boost the signal?"

"No. Tim's been trying but there's just too much going on."

"The Homo erectus are talking about some kind of weapon…I can't quite make it out yet but Colonel Sheppard should receive the information in real time." Moira sighed. "I should be on that ship with him," she muttered.

She recalled the argument she had had with John. She had been determined to go with him and he had been just as determined to keep her safe. A smile stole across her face as she remembered the passionate resolution of their argument. For some reason John would become aroused when they argued and the resulting sex was very intense and satisfying.

Chris sighed. "We're not a military installation! We were set up as a science unit, nothing more, until these new species came along. We can get a pretty good idea of what's going on out there, but beyond that..." He shrugged. "In any event we have to be careful in case the aliens somehow detect our scans and head this way."

"Aren't they a little busy right now?" she snapped, startled out of her sensual reverie. A blush stole across her face and she eyed her computer to conceal it.

"Yes…but Colonel Sheppard was quite explicit about that." Chris frowned and shook his head. He turned to a lanky redheaded man. "Dial Atlantis. May as well give them what little we have. Green, keep monitoring all frequencies. I know it's not your field but do the best that you can."

"Of course." Moira restored the headphones, hoping to hear the voice of her husband again, and praying that the translation program would give him every advantage.

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"Incoming wormhole!"

Rodney spun round in his chair as Chuck Campbell made the announcement. The chevrons lit one by one until the event horizon exploded outwards. The light was slightly off, as if dimmed by something or not entirely coherent. The shimmering pool was glazed over by the Shield.

"Confirming ID…it's Echo Base! Transmission!"

"Lower the Shield. Echo Base, what news?" Richard asked, stepping round to view the Stargate, although no one was coming through it. The vid-link wasn't working so he only had audio to glean what information that he could.

For all the advancements and technology there were still the age-old problems of equipment not working or being curtailed by interference.

"All of that firepower is wreaking havoc with our systems, but we can tell that the battle is being fought right now in real space." The man's voice crackled over the system. "Our estimates are that there are at least twenty to thirty ships total, theirs and ours."

"Have you made contact with Sheppard?"

"No. We were able to pick up some chatter between our ships, but that's all. There's too much interference for our scanners to dilute the-"

"Change your frequency!" Rodney suggested. He scooted to another console and began to type furiously. "I'm creating a program!" His fingers flew over the keyboard.

"We have. There is too much static and radiation."

"Try re-routing the power levels directly into the receiving discs! You should be able to boost your input significantly! I'm sending a data program now! Damn it maybe I should go to Echo Base and help them increase their output!"

"Keep us apprised. Woosley out."

"Whoa wait! I was going to—"

"We need to keep these contacts short," Richard stated, gesturing. The event horizon dissipated. The Stargate stood silent, empty. It had nothing more to reveal. Abruptly the vid-link crackled to life, only to reveal nothing but static.

"Do you truly believe that they could find us?" Teyla asked. There was a tone of alarm in her voice. Silence fell as all eyes turned to the expedition leader. Fear was a quick current running in the room. The very thought of the aliens finding Atlantis was chilling. They had come very close the last time, too close. The only thing that had prevented them from locating the city was the fact that it had been underwater at the time.

Richard exchanged a look with Rodney before meeting the Athosian's gaze. "Anything is possible." He eyed Chuck. "Keep those long-range scanners running and try to fix our Gate connections."

Nervously he glanced out the window to the blue, empty sky.

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There was a storm brewing. The wind was howling and it had begun to snow again. It was not an uncommon occurrence on the ice planet but the timing couldn't have been worse. Moira sighed and cursed, glaring at the screen. Static was replacing the scattered bits of information now, making her job all that more difficult; cutting her off from John even more.

It was aggravating and worrisome, having no idea what was going on out there. Anything and everything could be happening, and although she trusted in John's expertise and skill she could not help but worry about him. She knew the Homo erectus better than anyone. She knew they could be ruthless and cunning. She knew they could be dangerous and unpredictable.

Luckily John also possessed those same qualities.

"That's it." Doctor Tim Ironton moved to his feet as he crawled out from beneath a console. He wiped a smear of grease across his cheek. "I've done all that Doctor McKay suggested, but with this storm interference they could be right above us and we wouldn't detect it. Not that they would even come here but you know what I mean."

"You mean we're in the dark now. You mean that Sheppard and the fleet are on their own." Chris shrugged. "Keep monitoring. If any ship heads this way we need to know immediately. With any luck it will be our ships returning, although they aren't set to return here after the battle but return to a staging point and then to Atlantis."

"We don't have anywhere for a large ship to land. This base wasn't built for that," Tim noted.

"This place wasn't designed for anything like that," another scientist agreed.

"I'll keep monitoring if any transmissions get through," Moira offered. "There might be a break in the weather." It was a longshot but it was worth pursuing.

"Um, Doctor Sands? If in the unlikely event that the, the Homo erectus do happen upon us…" Tim swallowed nervously and felt a shiver that had nothing to do with the permanent cold of the planet.

"They won't. And if they do we can exit through the Stargate unless there isn't time."

"Can we? The Gate hasn't been working correctly for some time. It would be an awful risk going through it," Tim cautioned.

"We aren't going anywhere," Moira argued. She was not about to leave the planet unless John was with her.

"I know. It's a worst case scenario. In that case we have deeper underground bunkers that we can access. I am more concerned about any residual radiation hitting us from the outcome of the battle. Depending upon the extent of an explosion or a weapon's discharge either could negatively affect the atmosphere."

"Making a cold planet even colder," Tim muttered gloomily. "And God knows what that would do the wildlife here…and the indigenous species."

"All of our work could be for nothing," another mourned.

"We aren't leaving until we know that John, er Colonel Sheppard is safe," Moira stated firmly again. "As for the rest they'll be fine. They have survived countless Ice Ages."

"They have…but will we?"

The question hung unanswered in the cold air.


	3. Chapter 3

Stargate Atlantis: S7—The Species Divide3

It was time.

It was the only option, really. The enemy was relentless and powerful. Their weapons were inflicting damage. Already a few ships had been forced to fall back to effect repairs. The darkness of space was on fire with colored lasers zipping back and forth. The glow of shields filled the vastness and dimmed the light of the distant stars. The gas nebula marking the void between the two galaxies was a maze of red and blue mist, appearing to retreat and expand as the battle raged.

It was a gamble.

The options were few. The tide has been even but was now slowly turning against them. Several ships were reporting damage. The smaller fighters were swarming like hornets and doing their best in ship to ship combat. Eventually they would be rendered ineffectual as the larger vessels closed in for the kill. There was neither advancement nor retreat but soon that would change.

It was dangerous.

Power levels were increasing rapidly. The ships weren't built for such sustained combat, not at this intensity. The shields would begin to lose power first, failing under the constant bombardment. And eventually the weapons systems would fail one by one. So far nothing vulnerable had been targeted but it was only a matter of time. Alarms sounded and were shut down to be ignored at the moment.

They couldn't risk a direct hit that could render them useless or damage the hyperdrive systems. They couldn't risk becoming irreparably damaged because there was no rescue out here; there was neither safe harbor nor any planet upon which to land. Home was far away and out of radio range. Ships would either survive or die here.

As would the crews upon them.

Decisions had to be made, and made quickly. They were essentially alone out here, cut off from any higher authority. Whatever the outcome the praise and the blame would fall squarely onto his shoulders and he knew it. He knew what he had to do. There was no other option.

They might have taken on too much and underestimated the opposing forces. It had happened other times, but never had the stakes been so high. He had studied the attack and defensive maneuvers during the battle. Some of it made sense; some of it was incomprehensible to him.

The few encounters he had had with the aliens had only convinced him they were doing the right thing. They had always done the right thing under the circumstances. These aliens could be brutal and cruel. They squandered resources and had made no attempt at all to communicate or to broker any kind of agreement.

The aliens were scattering but seemed to be under the orders of one command ship. He realized that this was where the peril lay. He would have to make stern countermeasures to achieve victory.

The rules were clear. Nevertheless he felt the sweat on his palms. He swallowed, calming his voice before he issued the orders that would decide the outcome of this battle. Defeat was not an option. There was only one option.

He only hoped that he would be remembered for his bravery.

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"We've lost hull integrity in Section E, sir!"

"Outbound are reporting heavy losses!"

"_Flight One_ has had to withdrawal with heavy damage! She won't make it back!"

"Picking up transmissions but they are gibberish, sir!"

"Weapon capacity is at seventy percent and holding steady!"

"Detecting scans! Initiating blocking sequence!"

Another alarm blared, cutting off the voices all clamoring for attention. The ship shuddered and the shields flickered but held. Colors dazzled the eye as the viewport was a miasma of destruction and power.

Space was full of flying vessels and it was an awesome sight. Smaller ships careened and dove and blatted laser fire. Some spun out of control. Some swirled and swam amid the stars, pocked by explosions and failing systems. Others flew directly into their deaths, as if on some suicide mission only they knew about. Still others limped back towards the safety of the larger vessels, like chicks seeking the protection of the mother hen.

Except that some of the mother hens were sustaining losses now.

"Re-route all remaining ships. Destroy every enemy ship that you can. We're done here." He flexed his fingers, cracking his knuckles. It was a loud sound echoing on the bridge. "Execute order one one six two."

The silence was absolute. Even the ship seemed to hold its breath, alarms quieting and the buzzing of the bombardment momentarily halting. No one questioned him. No one said a word. Orders were orders.

Without another word he left the bridge. Quickly he descended several levels to the engineering decks. Security was tight here but he passed through with quick acknowledgements. Reaching the main chamber he paused to view the array of weaponry assembled.

He could feel the ship's power here. It was humming under his boots and seemed to reverberate in every step that he took. It was a song in his ears and the white noise crowded out all doubts, all concerns and all worries. Power was here and the power was his. He crossed to the main power grid and tapped the shoulder of a technician. "How long?"

The technician straightened immediately, startled. "About ten minutes, sir."

"Make it eight. They are moving too close too fast. Beaming technology?"

"It is limited as far as we can tell, sir, and only some vessels have it. The technology is different and based upon a different set of equations and—"

"Are we in danger of being boarded?" he snapped, cutting to the chase.

"No, sir!"

"Have you been able to isolate their drives?"

"Yes…but they are heavily protected. Only a direct hit would do any significant damage, and it would have to penetrate the shielding as well as the hull."

"That won't be a problem. We are going to annihilate all of them."

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The little blue light blinked, blinked. It was a soft, soothing blue, the shade of the sky as seen from a planet. He stared at it a moment, letting its color wash into his eyes, obliterating everything else. He stepped to the panel and set the code. His fingers slid over the key pad as he typed in the codes only he knew.

The blue light blinked once, twice. It shone with a steady glow now. There was no countdown. There was no voice telling him how long they had or when the weapon would be ready. It wasn't necessary. The deed was done, and there was no going back now. There was no reset. There was no way to abort this program once initiated.

It was a failsafe program, designed for the direst of circumstances. It was a program that could only be initiated once. Commitment was total. There was no going back once the sequence had been keyed into the system. No overrides exited.

It was the last resort.

He nodded and closed his eyes a moment, letting his thoughts settle and glide along his emotions. He had to find that inner peace, that acceptance of fate and destiny. At the same time he would savor the revenge for lost comrades. He would savor the revenge for the damage done to their precious ships.

He opened his eyes and returned to the bridge. Everyone was busy at their stations, working and continuing the battle. Although they were aware of the order they kept fighting. He felt a swell of pride. His crew were professional to the last, the very last.

It was time.

It was a gamble.

It was dangerous.

This battle would be ended once and for all, and every species involved would either submit, or die.

Every species involved in the fight.

Including the ones from Atlantis.


	4. Chapter 4

Stargate Atlantis: S7—The Species Divide4

"Everybody get outta here now! Disengage and get as far away as you can!" John was shouting orders as he ran across the bridge of the _Tria_. There was a cacophony of reaction and he ignored it all. He placed a firm hand on an airman's shoulder. "Keep us on course, shields at maximum. When I give the word you drop the shields."

"Sir?"

"Just do it! I am going to fire the Drones but I have to very precise, or none of us are gonna make it! The second I fire the Drones raise the shields and get us the hell out of Dodge! Understood?"

John didn't wait for an answer. He moved back to the command chair. "Get out of range now! All ships get out of range! They are going to blow everyone out of the sky!" His fingers flew over the control pad, initiating controls and causing a fluctuation of energy levels. The already overdrawn ZPMs were about to taxed to the extreme.

He shut off his earpiece, silencing the clamoring voices all demanding explanations. He hastened off the bridge and down to the engineering deck. It was hot down here. Power vibrated beneath his boots as he made his way towards the Ancient Control Chair. He could feel himself sweating and it wasn't from the oppressive heat.

The last words that had been translated had been truly chilling. Instead of a détente or a retreat the enemy was going to use another Penning trap device to destroy everyone—even themselves. John knew he had only one chance to stop this. He had only one chance to neutralize the threat, the same way he had when Atlantis had been in danger. Only this time he wanted to destroy the Fugly vessels as well.

Every last one of them.

John eased himself into the Chair. Instantly it responded, humming with power and reclining. Lights flared. John licked his lips. He closed his eyes as his hands slid down along the armrests. He knew he had to concentrate. He could feel the strange symbiosis of man and machine as his ATA gene gave him unlimited access not only to the Chair but to the entire ship's systems.

"Channel all excess power to me," he ordered. His voice sounded raspy and he swallowed, wishing he had a beer.

He took a deep breath and released it. He flexed his fingers. His timing had to be precise. Any miscalculation would result in disaster. He could hear McKay's voice in his head and he smirked at the remembered irate tone of his friend as he went on and on about the equations and mathematics. Luckily John had been paying attention for once.

Although the programs were mostly automatic once initiated John had to be precise and guide the missiles to their target with exact coordinates. Only he could control the timing and direction of the Drones so they would unerringly hit their target. Anything less would be a spectacular and deadly failure.

His thoughts briefly drifted to Moira. She was waiting for him. She was waiting to begin their life together, as was he. The months apart had been difficult for both of them. The separation had been necessary. Everything had led up to this. He wasn't seeking revenge for what the Fuglies had done to her. How they had ripped into her mind and caused her to have hallucinations. All the same it gave him satisfaction to end them once and for all.

If he couldn't have one of their ships he would annihilate the entire threat to the galaxy.

He would make the galaxy safe for Moira again.

John cleared his thoughts. He cleared his mind, drifting into the interface of man and machine. It was a giddy rush of power. He felt he was the ship, flying through space, enduring the repeated hits on the shield. He could feel the awesome vacuum of space and the distant stars. He could feel the immensity of this mission and the dire circumstances that had prompted it. He had to succeed where the Ancients had not.

"Shields drop on my mark. Remember my orders. Get us clear once I have fired the Drones. Is our fleet clear?"

"Yes, sir, mostly. There are a few stragglers and a Wraith Hive is—"

"No matter. Mark."

At his soft words energy evaporated around the _Tria._ Instantly the ship was bombarded. Explosions rippled along the hull. Alarms wailed. John ignored it all. He fell into the weaponry and fired the Drones. He felt he was flying with them; guiding them unerringly towards their intended target. He felt the rush of space all around him. He felt the sweat beading on his brow. He felt the surge of adrenaline as the Drones hit the shields. Some faltered but most got through, bolstered by the additions McKay had added.

He grunted, rocking in the Chair as if he could feel every blast, every laser that was bombarding the ship. He gritted his teeth as he felt the Drones hitting the Fugly ship, penetrating the hull with violent intent. He urged them on, on, on!

The yellow Drones swam forth into the Fugly ship. They ripped it apart as they sped to the engineering level. They tore apart the walls and shredded any nearby Fugly personnel. They wreaked havoc as they bore towards the array of weapons. They screamed as they tore into the Penning trap device. For a moment the twin explosions were neutralized, just as they had been at Atlantis.

There was a surge of power and the illumination was almost blinding. It was like staring into the heart of a star until it blinked out, wavering as negative and positive forces collided. Everything halted. It was as if time itself has stopped, holding its breath as the fragile balance between charged particles was suspended.

But then John drew back and directed the Drones off-center. He drew them just enough to negate the disastrous explosion that would have destroyed this quadrant of the galaxy. It was enough to create the massive implosion he needed.

BOOM.

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Rodney froze. His fingers froze on the keyboard and he stared at the screen in shock. He couldn't find his voice, a first for the usually voluble physicist. He could only stare at the scanner's readout in both dismay and wonder.

"My God…" Radek's voice was soft, full of amazement and concern. "We're detecting a massive energy output on the edge of the galaxy…in the same vector as…"

"Sheppard." Rodney swallowed. "It's an explosion comparable to that of a supernova."

"If our ships weren't clear—"

"They were clear. I also detected several hyperspace windows just before the explosion."

Richard joined the two scientists as they sat side by side, conferring quietly. "Any contact?"

"No. And it will be hours before we can detect anything, or before we receive any transmissions." Rodney sighed.

"An explosion of that magnitude would—"

"I know!" Rodney shouted, not letting Radek finish the rest of his sentence. Rodney sighed. "Sorry. Sheppard got clear. I'm sure they all got clear. I told him quite specifically how massive the explosion would be and what to do."

"Even so the resultant radioactivity would create a wave of disproportionate—"

"Stop being such a negative Nancy!" Rodney snapped. "I'm sure he got clear in time! He may be stubborn but he's not stupid!"

"I never said he was stupid. I was merely theorizing that the force of the—"

"Enough theorizing," Richard intervened. "Keep scanning. I'm sure Colonel Sheppard will contact us once he's in range. Monitor the rendezvous site as well."

"Of course." Rodney exchanged a look with Radek before both men resumed staring at their blank monitors.

XxX XxX XxX XxX XxX XxX XxX XxX XxX XxX XxX XxX XxX XxX XxX XxX XxX

The pain hit suddenly. It was a wave that knocked Moira like a punch. She cried out and swayed in her chair, touching her head where the headache surged. The area behind her eye where the neural implant had been was on fire, throbbing with a vicious tune that sounded like screaming.

Suddenly she was on the floor, grasping her head and biting her lips to keep the scream from erupting out of her mouth. Images filled her mind—images of the Homo erectus being torn apart and cut down like blades of grass by some unseen, violent event.

Voices were calling and she felt a hand on her shoulder. Tears filled her eyes and she couldn't respond.

Just as suddenly the pain was gone. A phantom remnant remained and she rubbed her temple, puzzled and alarmed. "I'm fine…I just…that headache came out of nowhere and just…" She stared as scientists were rushing out of the room.

Alarms were wailing.

Moira shakily stood, shaking her head and rubbing her temple. She ran into the control room on Echo Base. Her long ponytail flew behind her like a banner against her white lab coat. "What's happening?" she asked breathlessly.

Technicians were scrambling at the consoles, all clamoring at the same time. The screens were full of static and distortions. It was a scene of chaos as both machines and men were scrambling with bursts of energy and information.

"We've detected a massive explosion in the battle quadrant! All of our systems are being fried!"

"Shut it down! Shut it all down! The shock wave will overload everything!"

"Any transmissions?" Moira asked. Her heart was in her throat and her chest was pounding. John was out there, in the thick of it and more than likely the source of the explosion. He hadn't told her much about the details but she did know that the _Tria_ was equipped with a very powerful and very dangerous weapon to counteract the one the Homo erectus had.

"The last one was Sheppard ordering the fleet to get clear. After that, zilch."

Chris sighed. "We'll be blind and deaf for several hours. Anything in that immediate area of that blast zone is history. Give it an hour and then keep trying to monitor all frequencies, but as of now we are completely cut off."

"If that wave hits us when the other planet isn't shielding us…"

"I know. We could lose the Stargate."

"What?" Moira exclaimed.

"The electromagnetic wave will fry our systems and there is the possibility that it could also destabilize the naquada in the Stargate on an atomic level. Let's hope the planetary rotation save us this time."

Moira moved to stare at the monitor full of static. There was nothing she could do. There was nothing anyone could do but wait.


	5. Chapter 5

Stargate Atlantis: S7—The Species Divide5

"Colonel? Colonel Sheppard? Can you hear me?"

John's mind cleared. He had been lost in a fog, lost amid the vastness of space and debris. It took some effort to pull free of the interface and restore his mind to his body. He grunted and blinked his eyes as the Ancient Chair righted itself, powering down. "Status?" he managed to growl. It took a moment to restore feeling to his arms and legs.

It took a moment to become fully human again.

"Nearly all enemy ships destroyed, sir. We barely made it clear in time. We've suffered some damage but it's minimal. The hull is holding against the radiation and debris. We managed a short jump to escape the blast radius and there's a Wraith ship hailing us."

"Nearly?" John stood. He wavered a bit until he found his balance. The room was dark. Lights were blinking and John focused on them for a few seconds. Although not as intimate as the interface was in Atlantis it was still very powerful and consuming.

"A few managed to get clear of the blast zone and are hightailing it outta here. Orders, sir?"

John remained silent a moment. Traces of the destruction still reverberated in his mind. "Track those two ships," he decided, starting to walk at a brisk pace. "Give me all damage assessments. I want the numbers of those enemy ships that were destroyed. Make certain our fleet is away. And open a channel to that Wraith ship."

The bridge was like a hive of bees. Everyone was busy at their stations, buzzing all the while in conversations and updates. A few errant sparks flew from consoles but the ship was intact and working. John slid into the command chair, surveying the vast debris floating in space all around them.

Where there had once been an imposing enemy fleet now there was nothing. Space was littered with pieces of ships. Not a single one remained intact. Even the pieces were unsalvageable. John glanced at the translation program still attached to his command chair. The screen was blank. The cursor blinked and blinked but no words formed.

"Two Fugly vessels, sir, are heading for the nebula."

"Set a course. We're going after them."

"Sir?"

John scowled at the questioning airman. "Mopping up. We don't want to run into these guys again. We'll make it. Engage long range scanners and see if you can pick up any chatter." He looked over to see a light blinking, indicating the channel was ready. "This is Sheppard. We need to get after those remaining Fugly ships," John said, as the _Tria _began a graceful arc to pursue her quarry.

"John Sheppard," cooed a familiar voice over the com unit. "You seem to have single-handedly done what all of us couldn't do."

John felt a smirk forming on his lips. "Todd. How nice of you to stick around."

"I wanted to see if you survived."

"I didn't know you cared."

"Sir, they're powering up weapons!"

"What? Todd, whatever you're thinking of doing, don't! Engage the shie—"

The ship was rocked by a laser before John could finish his sentence. Alarms wailed. Immediately the ship veered off course and the shields surrounded it like a cape. Debris bounced around, harmlessly striking against the wall of energy protecting the _Tria._

"Fire at will! Get the—"

"They're fleeing, sir! Detecting a hyperspace window!"

"Sir! Systems are off-line! We won't make the rendezvous point like this!"

"We won't catch up to the Fuglies. Only the subsystems are online."

"Shit." John scowled, watching as the Wraith Hive ship darted into hyperspace. "What the hell was that parting shot for anyway?" he wondered aloud. "Are you sure we can't pursue?" He stared out the viewport as the _Tria _turned again, aiming for the fleeing enemy ships like a hawk.

"Negative, sir. We're losing power. One of the drives has been compromised. Weapons are offline as well. We can either go after them or return to Echo Base. We don't have the power to do both."

"Damn it," John muttered. He watched his targets become smaller and smaller, disappearing into the blue and red gaseous expanse of the nebula. He glared, as if he could will the ship to keep going, to keep running after the remnants of the enemy fleet. He glanced at the translation program but it was blank. The enemy ships were too far now to intercept any radio transmissions.

Debris was a hazard, littering space like an asteroid field. A few latent explosions created plumes of light that were quickly doused by the vacuum of space.

"Orders, sir?"

John was silent, hands clenched into fists as he wanted nothing more than to go after those last ships and obliterate the threat once and for all. He heard the clamor of alarms and the _Tria _was listing slightly, trying to compensate for the damage to one drive.

"Get us to Echo Base," he finally decided. "We can effect repairs there and check in with Atlantis. I'm calling this a win."

He settled back and closed his eyes.

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John wiped his brow and leaned slightly against the Jumper's flight panel as he sat at the controls. Effortlessly he piloted the little vessel from the _Tria _as she established a secure orbit around the frozen planet. John was alone, flying to Echo Base.

Snow plumed all around the Jumper as he descended into the atmosphere. Whiteness nearly obliterated every feature, but he could make out the stolid form of the Stargate. He flew past it and landed smoothly near the icicled building.

Quickly he exited the Jumper and entered the base, greeted by the leader and other scientists. He nodded at the congratulations and briskly made his way to the control room. "I need to contact Atlantis now. What's the status here?" he asked, brushing snow off his black clothes.

"Every system is offline except for life support and basic programming," Chris complained. "We should be able to dial Atlantis but I don't know how long we can keep the event horizon active."

"I'll only need a few minutes," John stated, looking round. He didn't see Moira and the wave of disappointment was palpable. He suppressed a sigh and waited impatiently.

The Stargate lit up, the chevrons shining one by one as the address was dialed. The KAWOOSH lit the room and the snapped back to a shimmering pool. Static crackled.

"Atlantis, this is Sheppard. Do you copy?" John stood at the console in the Echo Base control room. Already technicians were getting ready to board the _Tria_. They would work steadily to repair the battered spaceship. "Atlantis, do you read?" He raised a brow and glanced at the station's leader.

"Sorry, colonel," Chris apologized with a shrug. "Our connection has been spotty at best, as you know. The residual radiation from the battle only made things worse. At least we are still in the shadow of the sister planet."

"Sheppard? You….we detected a massive….you didn't…sandwich?"

John smiled at the voice of Rodney. "Rodney! Yeah, that was me. Threat is eliminated. Repeat, threat is eliminated! Did the fleet make it to the rendezvous point?"

"Good to hear from you, John! Yes, the rest made it. What did you do to my ship?"

"Our ship and it's nothing we can't fix out here. I'll be back to Atlantis in about a week or so once the _Tria _is repaired."

"Repaired? What did you to do to….hyperdrive….no scratches on…"

"McKay? McKay, do you read?" John scowled as static filled the air. Abruptly the event horizon winked out of existence, cutting off all contact.

"Sorry about that, colonel. That's the best we can do for now and the resultant—"

"John! John!"

John smiled, irritation forgotten. He turned and found himself engulfed in a hug. He returned it, pressing Moira close to him and letting her love wash over him.

"John! Thank God! Are you all right?" Moira drew back, anxiety on her face. "You look exhausted! Was it the interface? That explosion…you took out the entire fleet? Did the translation program work? What happened out there? Did you—"

John cut off her words with a lengthy, sloppy kiss. He drew back, smiling, ignoring the embarrassed stares and speculation around him. "Later, Moy. Right now I could murder a burger and a beer." He slid his arm around her waist and began to draw her out of the control room. "Keep scanning, just in case," he called over his shoulder, "and keep me updated on the progress of those repairs. And try to re-establish a connection with Atlantis."

"Um, sorry about that, John…I mean I only just heard and—" Moira began, flustered.

"Don't worry about it, baby. The cat's outta the bag now. Doesn't matter anymore. It's over, Moy. All of it."

"Over? What does that…" She touched her temple suddenly, recalling the flash of pain. "You killed them." She freed herself, staring at him. "You killed them all."

"Nearly all. Two ships got away and we couldn't pursue. What?" he asked to her accusatory expression. "It was kill or be killed. They were going to initiate their Penning trap and not only obliterate us but themselves as well! Your translation program told me that!" he stated, pointing at her. "And thank God it did. I got everyone clear in time then made sure that this ended. That's my job, Moira. It couldn't end any other way. Wait…you…you felt that?"

She nodded. "I felt…something but I didn't know what it was. It's probably a residual effect of the neural implant. No…I'm fine." She held up her hand, forestalling his advancement. She stared at nothing for a moment, as if she could hear the ghostly screams of the dead. "Let's get you something to eat. How long will you be staying here?" She began to walk away from him.

John followed, puzzled and annoyed by her reaction. "A week, I guess. I dunno. It all depends on the state of repairs. Moy, I didn't know you would sense that. Should I call you Obi-wan now? Moira? Moira!"

She slowed and turned to him. There were tears in her brown eyes. She stepped to him and hugged him. "It was…it was horrible, John! The pain, the despair, the inevitability…and I thought…I thought I lost you," she whispered, hiding her face against his shoulder.

John relaxed and held her close. He kissed the top of her head. "You will never lose me, sweetheart. It's all right. I never thought you would feel any of that. There was no other course of action. Let's grab some food and go to your room, all right? Moira?"

She freed him. She kissed him, a slow, sweet kiss that whispered of passion. "All right, John. It's just us now, right? For a little while it can just be us, here." She took his hand and led him towards the transporter.

"It's just us here, now…and then Atlantis," he quietly corrected.


End file.
